Horrible Doctor Cooper
by Darkly Dreaming
Summary: AU inspired by Dr. Horrible's Sing-A-Long Blog. Sheldon decides to get revenge after the Arctic expedition with Penny as his partner in crime. Rated T. Warnings: violence, vengeance, and major character harm. COMPLETE.
1. Act I

A/N: If Sheldon seems a bit OOC it's because this is AU, and being AU, everything is the same, but a little bit different. Here, the story deviates at the Comic-Con line. Sheldon is just a tiny bit more receptive to touch, but not that much. Just enough to make it a little easier to write, but still be Sheldon. I hope you understand, and don't flame me for Sheldon being OOC. This also happens to be a universe where Sheldon dances and only drinks hot chocolate in months with three vowels, although you won't see that.

* * *

His friends say he's only one lab accident away from being evil.

If only they knew the truth.

It's true that Sheldon Cooper, Ph.D. is a scientific genius and a social cripple.

It's also true that he's trying to prove String Theory.

But he's far from innocent. The only reason his death ray hadn't worked wasn't because of the lack of materials - it was because it wasn't _supposed_ to be a death ray. It was _supposed_ to be a phaser modeled from Star Trek, and it _would_ have worked with a little bit more tweaking. In fact, it had. Right before he left for college at eleven a kid had mysteriously fallen into a coma - the last bully he'd had to endure before leaving. He never woke up.

He now has a phaser rifle and a laser pistol hidden with his 9mm in his apocalypse gear.

He can also lie fairly convincingly. He could suppress his facial tics, but most of the time he had no reason to lie, so around his friends he didn't bother to hide.

And he was in love with his neighbor Penny.

Unfortunately, Penny seemed to completely overlook him in favor of Leonard. The snuggie said it all.

When they went to the magnetic North Pole and he proved String Theory he'd prove to her that he was worthy of her affection as well as his Nobel.

There was only one problem with his plan: Leonard.

Leonard and the others had sabotaged his entire experiment, falsifying data in lieu of killing him out of frustration. Leonard was supposed to be his best friend, so of course he was completely blind-sided. He wasn't surprised by Howard or Raj - Howard had the look of a henchman at best, and Raj always followed Howard - but Leonard was a scientist and his best friend. His roommate. He knew what he was getting into - they all had. The personal betrayal stung, of course, but the professional betrayal hurt worse. He would've preferred that they had retaliated physically. Attacking his work was below the belt, as the saying went.

Moths are too good for them. Leonard was going to suffer.

As Sheldon lie curled up on his bed plotting, Penny walked in and sat behind him. "Hey. Do you wanna talk?"

"About what? Being betrayed by my friends? Spending three months at the North Pole for nothing?" He paused a moment. "I would've dressed as the Joker for Comic-Con, had I been able to go. Not Heath Ledger's Joker, Jack Nicholson's Joker."

"I'm sorry, sweetie. You don't deserve what they did to you. No one does." Penny couldn't resist anymore and squeezed his shoulder, withdrawing quickly lest he complain.

"For a while I've been thinking about grinding moths up into Leonard's food," he softly intoned, listening for Penny's reaction before continuing. She was a little weirded out and uttered a tiny moue of disgust, but thought 'That's not too bad considering what Leonard had done to him.' Then he continued.

"But he deserves something more for this." There was a hardness underneath the soft whisper, a steely sort of conviction.

"Sheldon?"

He sat up and faced her. In a low voice he asked her, "Penny, what if I told you I wasn't exactly the innocent you all think I am?"

"What do you mean?" Penny should've been worried by his words, but his eyes craved her trust after his betrayal and she wasn't about to abandon him.

"The others have said I'm one lab accident away from becoming a supervillain, but they're wrong. If one knew of my past, they might say I am already one."

Penny was concerned, of course, and still a little confused, but willing to hear his story. "What happened in your past, Sheldon?" She refused to use the words 'evil' or 'supervillain' until she's heard the truth.

"I haven't told anyone about any of this." His eyes were so intent. For a man who claimed he didn't have emotions, his eyes were incredibly expressive. "You have to promise me you won't tell anyone."

She was about to agree when there was a knock at the door. Penny answered it, and when she saw Leonard with his hurt puppy look she about slapped him. Instead, she hissed at him to go away and slammed the door in his face. She snarled - that was the only word for it, he thought - and her junior rodeo showed. "All he wants is sex, the pathetic little -"

"I call him a pathetic myopic homunculus."

"I was gonna go for 'pathetic little shit' but that works too, I guess." Then she thought. "Myopic is near-sighted, but what's a homunculus?"

"Perfectly formed miniature human."

"If he's a perfectly formed miniature human then why is he myopic? And lactose intolerant?"

"You're right," he nodded. "Homunculus is too good for him. We'll stick with 'pathetic little shit.'"

Penny sat back on the bed and crossed her legs in front of him. "Tell me about your past, Sheldon. I wanna know."

Sheldon took a deep breath and began.

"I was bullied as a child, you can imagine. I was a prodigy. Others were jealous, or just hated my arrogance, but instead of ignoring me they bullied me. I had started watching science fiction shows by then, as an escape from reality. Star Trek, as you know, was my favorite. After coming so close to creating a working CAT scanner I thought a phase gun or laser gun wouldn't be too hard. My father had a few guns when I was small, so I stole one of them and took it apart, figuring out how it worked, and how I could possibly make a phase pistol or laser pistol with the design.

"After the encounter with the government over the yellow cake uranium, I found another way to do it using spare parts from old tvs and radios and other such junk, and, of course, my father's handgun. I now have a working phaser rifle and laser pistol along with the Beretta I bought when I moved here.

"If you look through Galveston's past newspapers you'll see an article detailing the hospitalization of a coma patient. A fifth grader. He was the last boy to bully me before I left for college. The doctors' best guess was electrical brain damage, but couldn't find the cause. It was the first test of what my mother had called a death ray, but was really the prototype for my phaser rifle. He never woke up."

Sheldon paused to catch his breath and let the information sink in before he continued.

"When I was fifteen a fellow researcher saw my work and thought himself superior to me - by which I mean he tried to steal my work and pass it off as his own. He also fell into a mysterious coma, but died shortly after of a heart attack that was only partially my fault. He had a weak heart and my phaser was a catalyst. A month later I won the Stevenson Award."

"So that Nowitzky chick got off easy, huh?" Her voice was a little shaky, but finding out your friend had kind of killed a guy at fifteen and put a kid in a coma at eleven would do that to you. Sheldon was relieved, though. She hadn't run from the room screaming his indiscretions. Joking was a start. The corners of his mouth twitched up. "She didn't deserve my wrath, merely my rejection. After all, if it weren't for her I wouldn't have reached my conclusion as quickly. She just wanted to share credit for something she didn't do, she didn't want it all for herself. Besides, by now everyone should know that I don't share credit." Then he winked and smirked, both of which startled her and put her at ease simultaneously. She made the decision to be behind him 100% right then. She cared about him and it seemed like he only let out his dark side when he was wronged. She wouldn't call that evil. Vengeful, maybe, but not evil.

"So what are we gonna do about Leonard?" she asked with open and supportive eyes.

Sheldon felt hope bubble in his chest. "We?"

Penny nodded and smiled. "Yes. We. You are my friend and friends don't abandon each other. Plus, I kinda like the idea of being the femme fatale partner to your supervilliany." She winked. "With your tall, dark, and handsome genius and my curvy blonde sensuality we'd make quite the duo."

"Tall, dark, and handsome?"

"Well yeah, it's kinda hard to miss. Tall, pale skin, dark hair, ice blue eyes, and that intelligence? Haven't you heard smart is the new sexy?" She grinned, indicating that she agreed with the statement. "I was going to settle for Leonard, but why settle when I could go right to the top and snag the Joker himself, Sheldon?"

His brain was sifting through thoughts at a mile a minute. Was Penny actually attracted to him? Could that happen? The odds were very miniscule, but existent. He was never good with facial expressions, or emotions in general, so he just decided to ask.

"Penny, are you attracted to me?"

"Since the day we met, Sweetie. Like I said. Tall, dark, and handsome, beautiful mind genius guy. What's not to like?" Open, honest eye contact, dilated pupils, she was telling the truth. And now she was looking at his lips.

"I have an idea," Sheldon said after studying her. He harbored feelings for her as well and planned to use them to his advantage in their plot, if she was willing. "Leonard called 'dibs' on you when we first met. I was going to concede your affections to him, should he be able to elicit them, but Leonard can go to my mother's Hell." Penny looked offended that someone would actually call dibs on her before they had even spoken. "Penny, would you be my girlfriend as well as my partner in crime? Not only would it please me, but it would also serve in our revenge plot."

Penny was taken by surprise. She didn't think he saw her that way. Her disbelief showed. "Sheldon...I didn't think you saw me that way." She ducked her head a moment and came back up smiling. "I would love to be your girlfriend, Sheldon. But you do realize it'll involve touching, right? And you're okay with that?"

He nodded and smiled. "I am more than okay with touching you, Penny." As if to prove so, he ran his finger across her jawline and swiped her lower lip with his thumb. Her eyes fluttered closed and she leaned into his touch. "Can I kiss you, Sheldon?"

His lips on hers was her answer.

And that's what Leonard saw when he peeked through Sheldon's door. His Vulcan hearing had registered the door opening, but had ignored it in favor of kissing Penny. He pulled away after a moment and flicked his eyes at Leonard, letting him know he was caught.

"Ok, but if we're going to date," Penny said, also feeling someone watching. "You have to get rid of that beard. It adds to the evil factor, but it tickles."

Sheldon laughed his breathy laugh and agreed.

Penny moved to sit next to him and put her arms around him, laying her chin on his shoulder.

"Ok, sweetie, first things first. Damage control." She was about to ask about what he'd done with the false data and how he could recall it as gracefully as possible, but there was a timid knock on the door.

Sheldon opened the door to Raj. He looked distressed, like he was struggling to fight an inner battle. His eyes swiveled from Sheldon to Penny, still sitting on his bed, and back to Sheldon. Knowing Sheldon disliked whispering in his ear but not knowing any other way to communicate, Raj beckoned Sheldon out into the hall.

Sheldon nodded and turned back to Penny, who nodded for him to go. It was obviously important.

After the door closed behind them Raj spoke, eyes on his shoes. "I am so incredibly sorry, dude. We knew what we were getting into and we shouldn't have tampered with your work." He looked him in the eye and even Sheldon could see remorse in his expression. "I'm not apologizing for everyone else. They said they weren't going to, that they were just going to forget about it and hope we could move on, but I feel terrible, Sheldon. I'm going to tell President Siebert that it was our fault. This won't ruin you."

Sheldon was surprised. He was filled with such gratitude for the astrophysicist that he did the only thing he could think of to thank him. Sheldon hugged him.

"Thank you, Raj."

"If you wanted revenge I wouldn't blame you," he said after Sheldon stepped back. "But I would ask that you go easy on me. And give Leonard hell."

"Noted," Sheldon replied. "I will leave you out of it as long as you do not inform them of any of this." His eyes were hard again. "I want them completely unaware of what's coming."

In that moment Raj was incredibly glad he'd apologized. It looked like they'd caused that lab accident.


	2. Act II

A/N: I was going to wait until Wednesday afternoon to post this, but I can't stand myself any longer. I need you guys to have this. It is now one hour into Wednesday for me, so here you go! The second act deals with Howard who, despite his resemblance to Moist, is _not_ someone Sheldon considers a friend, or even a treasured acquaintance, anymore. It's considerably shorter than the first, and for that I apologize, but I think it works better this way. I also apologize for the lack of Penny. It's mostly a Sheldon story, with Penny supporting him. Hope I don't disappoint.

* * *

Sheldon and Raj visited President Siebert in his office first thing the next morning. Raj explained what had happened, suggesting, but not outright telling him, that it had been Leonard's idea. When asked what he had wanted to do about it, Sheldon had told him very succintly, and very humbly, "I just want to get on with my work and forget about it. Don't tell them we came to you, it will only cause more trouble. I've emailed you the correct experimental data. Perhaps there is still something we can glean from the negative results."

A week later and it seemed everything had returned to normal.

The engineering department was still a little wary of Howard ever since the space toilet debacle. They made him double and triple check everything he worked on, and the truth was, Howard himself had started doing that before they'd even mentioned it. He joked about a lot of things, but his work was very important to him. It was a point of pride in his life. It hurt when people doubted him, but he understood and worked every day to regain their trust and respect.

And Sheldon knew this because he felt the same way at the moment.

He told the others he was eating lunch in his office so he could keep working, and not a tic showed on his face. When the hallway was clear he walked to Leonard's office. It was a warm day, so he'd taken his jacket and hoodie off. Sheldon put it on, zipped it, and threw the hood over his head. Head bowed, he pulled on a pair of latex gloves, calmly strode into Howard's lab the JPL, and without turning on the light, unplugged the two cameras. Like with his Vulcan hearing he had very good eyesight, even in the dark. Once the cameras were unplugged he turned the light on and looked around. His eye caught the robotic arm Howard was building and he smiled.

It took a few minutes, but Sheldon found and rewrote the program so that when Howard input his password (_Really, Howard? Turbriskafil?_) the arm would grab hold of him as part of the startup program. He set the height at 5 feet 1.7 inches, and once the hand mechanism gripped it would rise a foot. If everything went to plan, the robotic arm would grab him at the throat and raise him up. Of course, the people he worked with could just unplug the computer from the arm and it would release him, but engineers rarely ever utilized Occam's Razor. They would likely try to disarm it using the program. It would take around six minutes for them to do so, during which time Howard would be losing oxygen, causing him to pass out. If his colleagues failed, he'd be dead. And just as well. Raj had also told him of Howard's crossbow.

Sheldon believed in nothing if not reciprocity.

He turned off the light, plugged the cameras back in and left. Before he returned Leonard's hoodie he carefully went over it with a lint roller to remove any hairs that might've stuck, then slid back into his office with no one the wiser.

The next day Howard was rushed to the hospital due to oxygen starvation and a bruised trachea. He wouldn't be talking for a while. The JPL found the problem with the arm and fixed it. Howard was not blamed, as it was clear it was sabotage, but no one knew who it could've been.

Sheldon offered well-wishes along with everyone else, but Penny knew and, while no one could prove it, Raj was sure it had been his doing.


	3. Act III

A/N: Sorry guys, meant to post this yesterday but I stayed up all night reading _Heat Rises_ and then I went to a gun show with my dad (still gunless, tho, those things are expensive and I have tiny hands *sadface*) and when I finally got home at 6 I passed the fuck out. So here's the last chapter!

Enjoy!

* * *

An investigation had been launched to find the robot hacker. Sabotage on anything for NASA couldn't go unpunished. The FBI crime scene unit combed the place inch by inch, corner to corner, but found nothing out of the ordinary; fingerprints all matched employees who had been ruled out by alibis or lack of motive. A specialist was going over each hair found, matching it to each person. There weren't many, but DNA evidence took a long time to process, despite what tv leads us to believe.

The allotted time passed and the results came. A single hair was found that didn't match any of the JPL employees. President Seibert ordered the entire Cal-Tech staff to submit to DNA testing, and Sheldon felt a tiny tendril of fear snake through him. Maybe he hadn't been as careful as he'd thought. He knew he'd avoided the cameras, but it's possible a hair had escaped the hood. He acquiesced, all the while reassuring himself.

He needn't have worried. When the FBI pulled Leonard in for questioning Sheldon knew what had happened. One of Leonard's hairs from the hoodie must have dislodged and fallen to the floor. Sheldon was once again in the clear, as they say.

Leonard was harassed by the government for days before they let him go. Sheldon listened to his complaints and relished the psychological damage being done. It hadn't been part of the plan, but Sheldon was willing to relish it all the same.

~*DD*~*DD*~*DD*~

_(This scene is brought to you because of Risknight. I had this thing finished, but she said something about a squirming Leonard scene and I just - I had to. Ask and ye shall receive, my dear.)_

Leonard sat in the cold aluminum chair, hands cuffed together, wearing a white jumpsuit. He'd been in this spartan room for hours now. They had given him a glass of water when he arrived, told him to sit tight, and that the agent would be there in a while. He had to go to the bathroom, but he was too scared to ask. What was his hair even doing in the JPL? The last time he'd visited Howard in the lab was weeks ago. Surely the janitors swept more often than that?

Suddenly the door opened to a tall, beautiful brunette with stunning eyes and an even more stunning figure. As beautiful as she was, she was that much more intimidating with the scowl on her face. She was quickly followed by a guy who looked like a body guard, or a bouncer, but had the same kind of badge on his hip as the woman.

"Hello, Dr. Hofstadter, my name's Special Agent Katic, this is Special Agent Huertas. Let's start by telling us why your hair was found in the JPL when only employees are allowed in the lab?"

Leonard could barely think straight. The need to urinate conflicted with his self-preservation and skewed his focus. The effect the agents saw was a very skittish and conflicted looking man.

Special Agen Katic opened a folder, presumably his record. Leonard briefly felt relief at how small it was, but felt that relief drop out of his stomach as dread replaced it.

"Whatever happened to that rocket fuel you were working on, doctor?" she asked, calm as can be. "Did you give it to Joyce Kim before she was deported?" Leonard was close to panicking, and close to wetting himself. Probably the effect they were going for.

"I TOOK IT HOME TO SHOW MY FRIENDS BUT MIXED IT WRONG AND BLEW UP THE ELEVATOR IN MY BUILDING!" He was near tears now, but continued. "I'm sorry, I didn't mean for it to happen, but I just wanted my friends to think I was cool. But I swear, I had nothing to do with Howard! He's my friend! I would never hurt him!" Sheldon's face flashed behind his closed eyelids and he realized the truth of what he'd done. He'd hurt his best friend. Special Agent Huertas, standing silently in the corner of the room, movied forward to say something, but was interrupted.

A knock at the door signalled his lawyer's arrival.

"You can't interrogate my client about an incident that happened years ago and has nothing to do with this case. You have nothing and you know it so you're fishing. Leave. Let me speak to my client alone."

Special Agent Katic nodded and stood. "We'll be back. Don't skip town, doctor."

~*DD*~*DD*~*DD*~

Patience is a virtue, and one Sheldon employed often. Two weeks after the incident the feds gave up. The case was cold. A week later Sheldon entered the experimental physics lab. This room only had one camera, which he hacked into and put on a ten second loop. Free to do as he pleased until lunch was over, Sheldon started tweaking things. It was only Leonard and Leslie in the lab today, and Sheldon didn't care what happened to Leslie. She was a bitch who believed Loop Theory. She deserved whatever happened just as much as Leonard for all the mocking and teasing over the years.

As it was, Leslie was in the bathroom when the laser exploded.

Sheldon had rigged the laser display to show only a fraction of the output, so when Leonard had dialed it up to 4 it was really 3x that.

The cube he had intended to heat melted and the laser itself overheated and exploded. Shrapnel flew everywhere. One piece embedded in Leonard's clavicle and another gashed the side of his head, knocking him unconscious. A larger piece hit a chemical cabinet, breaking vials of corrosives. Some of the chemicals mixed and ate the metal, and others emitted a noxious gas that quickly filled the room.

Finally, the smoke from the laser set off the fire alarm and sprinklers, drawing people to see what was wrong.

Leonard was rushed to the hospital. They bandaged the shrapnel wounds and treated the poison gas inhalation as best they could, but he was comatose for almost two weeks, during which time his friends visited often, but Sheldon and Penny only visited once.

"Some coma patients can still hear the things around them," Sheldon told Penny. "I can only hope that's true. I want him to know it was me." He leaned close to Leonard's ear and whispered. "Don't ever mess with my work, Leonard. You will not come out ahead. Be glad it wasn't worse."

Penny watched him threaten his ex-best friend. She knew she should probably feel bad for Leonard, but she just couldn't bring herself to feel anything but satisfaction. And seeing that satisfied look in Sheldon's eyes, like cold fire, did things to her. Penny thought of a different act that could put that look on his face.

"Sheldon," Penny tugged his hand. "Let's go home. We can go to comic book store later. There's something I wanna do first." The look in her eye left little doubt as to what it was she meant, and Sheldon was eager to agree. It seemed the satisfaction of conquering his betrayers left him hungry for more.

And he knew just what to consume to slake his hunger.

~*DD*~*DD*~*DD*~

Three days after Leonard woke from his coma and the second day he'd been home, the FBI had returned with a warrant for his arrest in the jet fuel case they'd just reopened. He looked over at Sheldon, typing on his laptop, and could've sworn he saw a smirk on his face. It reinforced the niggling thought that Sheldon was behind everything. He'd had a nightmare while in the hostpital that Sheldon stood over his bed with a knife to his injured clavicle, whispering about messing with his work.

Leonard was charged with theft of government property and reckless endangerment regarding the jet fuel. Sheldon couldn't have been happier. It was an unforseen side effect of his revenge, but he and Penny were more than willing to relish it.

Penny came over that same day and wrapped her arms around Sheldon's middle. "So, Howard's throat's better. Halo night? We've still got four people." She smiled and Sheldon could deny her nothing.

"As long as you're on my team I'm up for anything."


End file.
